The invention discloses a water supplementing and draining system and a method of a ship compartment of a ship lift, The system comprises a water supplementing and draining pipeline system, a water supplementing and draining butt joint device and a ship compartment, wherein the water supplementing and draining pipeline system comprises a main pipeline, a water inlet main valve, a plurality of electric control valves and a water draining main valve; the water supplementing and draining butt joint device comprises a lifting mechanism, a butting mechanism, a communicating pipe, a control cabinet,a signal transmitting end and a pipeline fixing mechanism; the butting mechanism is positioned on the lifting mechanism, the lifting mechanism acts, and is used for ensuring that the butting mechanism is kept consistent with the electric control valves with which corresponding heights; the butting mechanism acts, and is used for completing the butt joint of the water supplementing and draining butt joint device and the water supplementing and draining pipeline system; and the ship compartment comprises a ship compartment structure, a check valve, a water pump, an electric control valve I, anelectric control valve II, an electric control valve III, an electric control valve IV, a branch pipeline and a ship compartment pipeline. According to the water supplementing and draining system andthe method of the ship compartment of the ship lift, operators are reduced, time is saved, potential safety hazards are eliminated, the automation degree is high, and the integrated reliable operationof supplementing and draining can be realized.